RetrogeneDB ID: retro_tbel_883

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_3231:321105..321502(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: PCMT1
• Ensembl ID: ENSTBEG00000000451
• Aliases: None
• Description: protein-L-isoaspartate (D-aspartate) O-methyltransferase [Source:HGNC Symbol;Acc:8728]

Sequence

>retro_tbel_883
ATGGTCTGGAAATCCGGCAGCGCCAGCCACTCGGAGCTTATCCACAATCTCCGCAAAAATGCAATCATTAAGACAGATAA
AGTATTTGAAGTTATGCTAGCTACAGACCGCTCCCACTGTACGAAGTGTAACCCATGTATGGGTTCTCCACTATCAGTAG
GTTTCCAGGCAACAATCAGTGCCCCACACATGCTTGAGTAGGCACTAGAACTTCTATTTGACCAAATGGCATGAAGGAGC
TAAAGCTCTCCATATAGGATCTGGAAGTGGAATCCTTACTGCATGCTTTGCACAAATAGTTGGATATAGTGGCAAAGTCA
TAGGAATTGATCACATTAAAGAGGTAGTAAATGACTCAATAAATAACCTCAGAAAGGATGATCCAGCACTTCTGTCC

Alignment

ORF - retro_tbel_883 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.71 %
• Parental protein coverage: 57.89 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAWKSGGASHSELIHNLRKIGIIKTDKVFEVMLATDRSHYAKCKPYMGSPQSIGFQATISAPHMHAYALE
          M.WKSG.ASHSELIHNLRK..IIKTDKVFEVMLATDRSH..KC.P.MGSP.S.GFQATISAPHM...ALE
Retrocopy MVWKSGSASHSELIHNLRKNAIIKTDKVFEVMLATDRSHCTKCNPCMGSPLSVGFQATISAPHMLE*ALE

Parental  LLFDQL-HEGAKALDVGSGSGILTACFARMVGCSGKVIGIDHIKELVDDSINNVRKDDPALLS
          LLFDQ..HEGAKAL..GSGSGILTACFA..VG.SGKVIGIDHIKE.V.DSINN.RKDDPALLS
Retrocopy LLFDQM>HEGAKALHIGSGSGILTACFAQIVGYSGKVIGIDHIKEVVNDSINNLRKDDPALLS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_883 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_883 was not experimentally validated.

Homology

Retrocopy orthology:

Tupaia belangeri does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009230	1 retrocopy	retro_cjac_75,
Macaca mulatta	ENSMMUG00000029462	1 retrocopy	retro_mmul_134,
Oryctolagus cuniculus	ENSOCUG00000000499	2 retrocopies	retro_ocun_871, retro_ocun_955,
Ochotona princeps	ENSOPRG00000002833	2 retrocopies	retro_opri_171, retro_opri_434,
Tupaia belangeri	ENSTBEG00000000451	1 retrocopy	retro_tbel_883 ,